scholarly journals Patterns of genetic structure and evidence of Egyptian Citrus rootstock based on informative SSR, LTR-IRAP and LTR-REMAP molecular markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Mohamed Abd S. El zayat ◽  
Ahmed H. Hassan ◽  
Elsayed Nishawy ◽  
Mohammed Ali ◽  
Mohamed Hamdy Amar
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Sweet Orange ◽  
Group Structure ◽  
Draft Genome ◽  
Species Level ◽  
Sour Orange ◽  
Group Level ◽  
Citrus Species ◽  
Citrus Rootstock

Abstract Background Releasing the draft genome of sweet orange provides useful information on genetic structure and molecular marker association with heritable breeding traits in citrus species and their structures. Last decades, microsatellite and retrotransposons are well known as a significant diverse component of the structural evolution. They represented the most potent elements for assessing sustainable utilization of the complicated classification in citrus breeding. Our study was performed to verify the structure analysis and the parentage genetic diversity among the Egyptian citrus rootstocks and the related species. Results Here, the performance of 26 SSR and 14 LTR-IRAP in addition to 20 LTR-REMAP markers have been used to conduct the discriminating power and the status of the genetic structure analysis among twenty specimens of citrus genotypes. As a result, the three markers approach exhibited a remarkable variation among the tested genotypes. Overall, the three markers have different discrimination power; the co-dominant SSR markers can differentiate within the group level only in addition to the species level of sour orange, while the dominant markers LTR-IRAP had the ability to discriminate among the group level in addition to species level and the origin of acids. Similarly, LTR-REMAP is suitable for classifying the group level and species level for mandarins as well the origin of Egyptian acids; probably due to it is integration of SSR and LTR-IRAP techniques. Structure and PCoA results of LTR-REMAP marker in strong support for the group structure of citrus species have been divided into four sets: acids, grapefruit/pummelo, mandarin/orange, and sour orange. Conclusion Our findings of the genetic structure analysis support the monophyletic nature of the citrus species; are able to provide unambiguous identification and disposition of true species and related hybrids like lemon, lime, citron, sour orange, grapefruit, mandarin, sweet orange, pummelo, and fortunella; and resulted in their placement in individual or overlap groups. The outcomes of these results will offer helpful and potential information for breeding programs and conservation approaches as a key stage toward identifying the interspecific admixture and the inferred structure origins of Egyptian citrus rootstock and acid cultivars.

scholarly journals CRISPR-based genome editing: Catching impossibles for citrus improvements

2021 ◽  
Vol 2 (1) ◽  
pp. 24-29
Author(s):  
Jagannadham Prasanth ◽  
◽  
Thirugnanavel Anbalagan
Keyword(s):  
Genome Editing ◽  
Public Perception ◽  
Sweet Orange ◽  
Draft Genome ◽  
Value Added ◽  
Citrus Species ◽  
Perennial Crop ◽  
Simple Task ◽  
Major Drawback ◽  
Daunting Task

Citrus is globally one of the major fruit crops, occupying a place of prominence in international trade and tariff through horticultural commodities. Despite such distinction, citrus crop is confronted with a variety of biotic and abiotic stresses, thereby, sustaining production is always a daunting task. The genome size of citrus is rather small, ranging from 265 to 400 MB, probably an advantage for controlled trait specific editing. The evolution of next generation sequencing has facilitated the whole genome sequencing of as many 10 citrus species with 16 draft genome sequences, offering near future possibility to develop genome tailored citrus species or inducing the desired genetic transformation to address the issues chronically ailing commercial citrus cultivation in India, which is by no mean, a simple task to accomplish. Despite genetically intrinsic challenges involved in generating transgenics in perennial crop like citrus, several transgenics have been developed in namely, sweet orange, lemon, and grapefruit loaded with some useful traits. But, the public perception and the time taken to develop trangenics in citrus and less success ratio led the researchers adapt alternate ways. Of late, the thumping success of genome editing tools, especially Clustered. Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has provided a new molecular tailoring machine for citrus improvement. In several citrus species like sweet orange, pummelo, and grapefruit CRISPR-Cas9 system has resulted in value added multiple traits-based transgenics. However, the major drawback of the CRISPR/Cas9 system is the generation of significant off-target cleavage sites as a result of complexing of gRNA with mismatched complementary target DNA within the genome. The use of CRISPR as genome editing technology is anticipated to induce many desired traits in citrus in years to come with more commercial applications in field for changed canopy structure, root traits, regular bearing, extended fruit maturity, besides multiple disease resistance.

scholarly journals Genome of a citrus rootstock and global DNA demethylation caused by heterografting

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yue Huang ◽  
Yuantao Xu ◽  
Xiaolin Jiang ◽  
Huiwen Yu ◽  
Huihui Jia ◽  
...  
Keyword(s):  
Sweet Orange ◽  
Epigenetic Modification ◽  
Epigenetic Modifications ◽  
Genetic Effects ◽  
Dna Demethylation ◽  
Poncirus Trifoliata ◽  
Protein Coding ◽  
Horticultural Crops ◽  
Citrus Rootstock ◽  
Methylome Analysis

AbstractGrafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years. Citrus plants, with a seed-to-seed cycle of 5–15 years, are among the fruit crops that were probably domesticated by grafting. Poncirus trifoliata, a widely used citrus rootstock, can promote early flowering, strengthen stress tolerance, and improve fruit quality via scion–rootstock interactions. Here, we report its genome assembly using PacBio sequencing. We obtained a final genome of 303 Mb with a contig N50 size of 1.17 Mb and annotated 25,680 protein-coding genes. DNA methylome and transcriptome analyses indicated that the strong adaptability of P. trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes. Heterografting by using sweet orange as scion and P. trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock. Single-base methylome analysis indicated that P. trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs (sRNAs) in scions compared to the level observed with autografting, implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting. Taken together, the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology.

scholarly journals Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1429
Author(s):  
Yang Teng ◽  
Jing Yang ◽  
Guofen Zhu ◽  
Fuli Gao ◽  
Yingying Han ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Haplotype Diversity ◽  
Botanical Garden ◽  
Source Population ◽  
Independent Evolution ◽  
Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

scholarly journals Genetic Structure Analysis of Three Hispanic Populations from Costa Rica, Mexico, and the Southwestern United States Using Y-Chromosome STR Markers and mtDNA Sequences

Human Biology ◽  
2006 ◽  
Vol 78 (5) ◽  
pp. 551-563 ◽  
Author(s):  
Rebeca. Campos-Sánchez ◽  
Ramiro. Barrantes ◽  
Sandra Honorato da. Silva ◽  
Michael. Escamilla ◽  
Alfonso. Ontiveros ◽  
...  
Keyword(s):  
United States ◽  
Costa Rica ◽  
Genetic Structure ◽  
Y Chromosome ◽  
Structure Analysis ◽  
Southwestern United States ◽  
Mtdna Sequences ◽  
Str Markers ◽  
Hispanic Populations ◽  
Y Chromosome Str

scholarly journals Suitability of Citrus Species as Hosts of Sphaeropsis Tumefaciens Hedges.

1969 ◽  
Vol 69 (1) ◽  
pp. 57-61
Author(s):  
S. D. Rodríguez ◽  
R. Rodríguez ◽  
P. L. Meléndez
Keyword(s):  
Disease Index ◽  
Sour Orange ◽  
Citrus Species ◽  
Disease Symptoms ◽  
Rough Lemon

The reaction of eight species of citrus and the chironja hybrid to inoculations with S. tumefaciens was evaluated in the greenhouse. All hosts developed disease symptoms, but their responses varied. Rough lemon was the host most severely affected by this pathogen, showing dieback symptoms 60 days after inoculation. The lowest disease index was observed in sour orange.

Sphaceloma fawcettii var. scabiosa. [Descriptions of Fungi and Bacteria].

1974 ◽  
Author(s):  
A. Sivanesan
Keyword(s):  
Geographical Distribution ◽  
New Caledonia ◽  
Sweet Orange ◽  
New South ◽  
Solomon Islands ◽  
Sour Orange ◽  
South Wales ◽  
Citrus Medica ◽  
Rain Splash ◽  
Satsuma Orange

Abstract A description is provided for Sphaceloma fawcettii var. scabiosa. Information is included on the disease caused by the organism, its transmission, geographical distribution, and hosts. HOSTS: Rough and sweet lemon, lime, grapefruit, sweet orange, mandarin and satsuma orange, citron (Citrus medica), C. japonica and C. jambhiri. Sour orange somewhat resistant (McCleery, 1930) or immune (51, 2478). DISEASE: Tryon's scab or Australian citrus scab. GEOGRAPHICAL DISTRIBUTION: Australia (Queensland, New South Wales), S.W. Pacific (New Guinea, New Caledonia (41, 85), Fiji, British Solomon Islands); probably New Zealand (Jenkins, 34, 516), S.E. Asia (Malaysia, Hong Kong, Sri Lanka), Africa (Malagasy Republic and Comores Islands (51, 2478), Malawi, Rhodesia and Zambia); South America (Argentina (33, 292)). (From literature cited and specimens in Herb. IMI: CMI Map 161, ed. 2, 1966.) TRANSMISSION: Presumably by wind and rain splash as in common citrus scab (CMI Descript. 438) infection arising at start of season from lesions on old fruits and twigs (McCleery, 1930).

Genetic Diversity and Genetic Structure Analysis of the Natural Populations of Lilium brownii from Guangdong, China

2009 ◽  
Vol 47 (7-8) ◽  
pp. 503-510 ◽  
Author(s):  
Yong-fang Huang ◽  
Mao-xun Yang ◽  
Hao Zhang ◽  
Xue-ying Zhuang ◽  
Xue-hui Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Natural Populations

scholarly journals Genetic structure analysis of Amblyomma mixtum populations in Veracruz State, Mexico

2019 ◽  
Vol 10 (1) ◽  
pp. 86-92 ◽  
Author(s):  
Mariel Aguilar-Domínguez ◽  
Sokani Sánchez-Montes ◽  
María Dolores Esteve-Gassent ◽  
Carolina Barrientos-Salcedo ◽  
Adalberto Pérez de León ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis
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